Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__MR1:200453 Length = 482 Score = 193 bits (490), Expect = 1e-53 Identities = 153/482 (31%), Positives = 231/482 (47%), Gaps = 43/482 (8%) Query: 4 KQQLLIDGAWVDGDAAR-FAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62 +QQ I+G W D ++ A T+P +G + + + A+AAA A P W + Sbjct: 10 RQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALTA 69 Query: 63 AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122 ER A + R+ E L + + LA + E GKPL EA+ EV ++ E E Sbjct: 70 KERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEV--------TYAASFIEWFAE 121 Query: 123 RARDI---------GDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKP 173 A+ I GD R ++ +P GV A P+NFP + PAL AG +V KP Sbjct: 122 EAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKP 181 Query: 174 SEQTPMTADLTLQCWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLL 232 + QTP TA AG+PAGV +++ G A +G + + + L FTGS VG L Sbjct: 182 APQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKL 241 Query: 233 HRQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHG 292 Q + K L+LELGGN P +V D + +AAV + + + + GQ C CA R+ V G Sbjct: 242 MAQCAPTLKK-LSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300 Query: 293 AVGDDLIDALTSAIAELRVAAPFSEPAPFYAGLT-----SVEAADGLLAAQDDLVARGGR 347 V D+ + L+ A+A+L+V AG+T + A + + + +D + +G Sbjct: 301 -VYDEFAEKLSMAVAKLKVG------EGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGAT 353 Query: 348 PLSRMRRLQAGTSLLSPGLIDVTGCD----VPDEEHFGPLLKVHRYRDWDEAIALANDTR 403 L+ + + G + P ++ T D V EE FGPL + ++ D D+ I ANDT Sbjct: 354 VLAGGKVHELGGNFFEPTVL--TNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTE 411 Query: 404 YGLSAGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSD--APFGGIGDSGNHRPSAYYA 461 +GL+A G + + + G+V N TG S APFGG+ SG R + Y Sbjct: 412 FGLAAYFYGRDISLVWKVAESLEYGMVGVN---TGLISTEVAPFGGMKSSGLGREGSKYG 468 Query: 462 AD 463 + Sbjct: 469 IE 470 Lambda K H 0.319 0.135 0.409 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 606 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 489 Length of database: 482 Length adjustment: 34 Effective length of query: 455 Effective length of database: 448 Effective search space: 203840 Effective search space used: 203840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory